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1.  Telomerase-Null Survivor Screening Identifies Novel Telomere Recombination Regulators 
PLoS Genetics  2013;9(1):e1003208.
Telomeres are protein–DNA structures found at the ends of linear chromosomes and are crucial for genome integrity. Telomeric DNA length is primarily maintained by the enzyme telomerase. Cells lacking telomerase will undergo senescence when telomeres become critically short. In Saccharomyces cerevisiae, a very small percentage of cells lacking telomerase can remain viable by lengthening telomeres via two distinct homologous recombination pathways. These “survivor” cells are classified as either Type I or Type II, with each class of survivor possessing distinct telomeric DNA structures and genetic requirements. To elucidate the regulatory pathways contributing to survivor generation, we knocked out the telomerase RNA gene TLC1 in 280 telomere-length-maintenance (TLM) gene mutants and examined telomere structures in post-senescent survivors. We uncovered new functional roles for 10 genes that affect the emerging ratio of Type I versus Type II survivors and 22 genes that are required for Type II survivor generation. We further verified that Pif1 helicase was required for Type I recombination and that the INO80 chromatin remodeling complex greatly affected the emerging frequency of Type I survivors. Finally, we found the Rad6-mediated ubiquitination pathway and the KEOPS complex were required for Type II recombination. Our data provide an independent line of evidence supporting the idea that these genes play important roles in telomere dynamics.
Author Summary
Homologous recombination is a means for an organism or a cell to repair damaged DNA in its genome. Eukaryotic chromosomes have a linear configuration with two ends that are special DNA–protein structures called telomeres. Telomeres can be recognized by the cell as DNA double-strand breaks and subjected to repair by homologous recombination. In the baker's yeast Saccharomyces cerevisiae, cells that lack the enzyme telomerase, which is the primary factor responsible for telomeric DNA elongation, are able to escape senescence and cell death when telomeres undergo repair via homologous recombination. In this study, we have performed genetic screens to identify genes that affect telomeric DNA recombination. By examining the telomere structures in 280 mutants, each of which lacks both a telomere-length-maintenance gene and telomerase RNA gene, we identified 32 genes that were not previously known to be involved in telomere recombination. These genes have functions in a variety of cellular processes, and our work provides new insights into the regulation of telomere recombination in the absence of telomerase.
doi:10.1371/journal.pgen.1003208
PMCID: PMC3547846  PMID: 23390378
2.  A study of two Chinese patients with tetrasomy and pentasomy 15q11q13 including Prader-Willi/Angelman syndrome critical region present with developmental delays and mental impairment 
BMC Medical Genetics  2013;14:9.
Background
The proximal chromosome 15q is prone to unequal crossover, leading to rearrangements. Although 15q11q13 duplications are common in patients with developmental delays and mental impairment, 15q aneusomies resulting in greater or equal to 4 copies of 15q11q13 are rare and no pentasomy 15q11q13 has been reported in the literature. Thus far, all reported high copy number 15q11q13 cases are from the West populations and no such study in Chinese patients have been documented. Dosage-response pattern of high copy number 15q11q13 on clinical presentations is still a subject for further study.
Case Presentation
In this study, we characterized two Han Chinese patients with high copy number 15q11q13. Using chromosome banding, high resolution SNP-based cytogenomic array, Fluorescence in situ hybridization, and PCR-based microsatellite analysis, we identified two patients with tetrasomy 15q11q13 and pentasomy 15q11q13. Both 15q11q13 aneusomies resulted from a maternally inherited supernumerary marker chromosome 15, and each was composed of two different sized 15q11q13 segments covering the Prader-Willi/Angelman critical region: one being about 10 Mb with breakpoints at BP1 and BP5 regions on 15q11 and 15q13, respectively, and another about 8 Mb in size with breakpoints at BP1 and BP4 regions on 15q. Both patients presented with similar clinical features that included neurodevelopmental delays, mental impairment, speech and autistic behavior, and mild dysmorphism. The patient with pentasomy 15q11q13 was more severely affected than the patient with tetrasomy 15q11q13. Low birth weight was noted in patient with pentasomy 15q1q13.
Conclusions
To the best of our knowledge, this is the first case of pentasomy 15q11q13 and the first study of high copy number 15q11q13 in Han Chinese patients. Our findings demonstrate that patients with tetrasomy and pentasomy of chromosome 15q11q13 share similar spectrum of phenotypes reported in other high copy number 15q11q13 patients in the West, and positive correlation between 15q11q13 copy number and degree of severity of clinical phenotypes. Low birth weight observed in the pentasomy 15q11q13 patient was not reported in other patients with high copy number 15q11q13. Additional studies would be necessary to further characterize high copy number 15q11q13 aneusomies.
doi:10.1186/1471-2350-14-9
PMCID: PMC3598341  PMID: 23320815
Chromosome 15; Cytogenomic array; Copy number; Pentasomy; Tetrasomy
3.  Migration of gastric cancer cells in response to lysophosphatidic acid is mediated by LPA receptor 2 
Oncology Letters  2013;5(3):1048-1052.
Lysophosphatidic acid (LPA), a natural phospholipid, is able to modulate diverse cellular responses through LPA receptors (LPARs). Several studies have reported that LPAR2 gene expression is increased in a variety of cancer cells, suggesting that LPAR2 is involved in gastric cancer. The present study investigated the expression profiles of the LPAR and involvement of the receptor subtypes in the LPA-induced migration of gastric cancer cells using cell migration assays, RNA interference, quantitative real-time PCR and western blotting. LPAR2 was observed to be highly expressed in SGC-7901 cells, a human gastric cancer cell line, while LPAR1 and LPAR3 were not. Transient transfection with LPAR2 siRNA was observed to reduce LPAR2 mRNA in SGC-7901 cells and eliminate the LPA-induced cell migration. It was also observed that LPA-induced SGC-7901 cell migration was inhibited by the inhibitor for Gq/11 protein and p38. The results suggest that the LPAR2/Gq/11/p38 pathway regulates LPA-induced SGC-7901 cell migration. The present findings suggest that LPAR2 may be a potential target for the clinical treatment of gastric cancer.
doi:10.3892/ol.2013.1107
PMCID: PMC3576385  PMID: 23426604
lysophosphatidic acid receptor2 (LPAR2); Gq/11; cell migration; gastric cancer
5.  Fatal pneumonitis associated with postoperative intensity-modulated radiotherapy in lung cancer: Case report and review 
Oncology Letters  2012;5(2):714-716.
Radiation pneumonitis (RP) is the most significant complication of acute treatment-related toxicities in lung cancer. Intensity-modulated radiotherapy (IMRT) with inverse planning enables us to achieve the desired dose distribution. However, there are many high-risk procedures associated with lung irradiation, including chemotherapy and surgery. We report a case of fatal treatment-related pneumonitis, where the patient had undergone postoperative IMRT for lung cancer. Following completion of radiotherapy, the patient developed progressive dyspnea. A chest computed tomography (CT) scan revealed the presence of diffuse reticular interstitial processes and honeycombing in both lungs. The fibrotic change in both lungs in a transverse view was compatible with low-dose irradiation of non-target organs at risk. Acute radiation pneumonitis was diagnosed. For patients receiving postoperative IMRT, low-dose irradiation volumes should be considered for lungs, as well as strict dose-volume histogram (DVH) parameters.
doi:10.3892/ol.2012.1053
PMCID: PMC3572979  PMID: 23420543
radiation pneumonitis; intensity-modulated radiotherapy; low-dose irradiated volume
6.  Mechanistic and Single-Dose In Vivo Therapeutic Studies of Cry5B Anthelmintic Action against Hookworms 
Background
Hookworm infections are one of the most important parasitic infections of humans worldwide, considered by some second only to malaria in associated disease burden. Single-dose mass drug administration for soil-transmitted helminths, including hookworms, relies primarily on albendazole, which has variable efficacy. New and better hookworm therapies are urgently needed. Bacillus thuringiensis crystal protein Cry5B has potential as a novel anthelmintic and has been extensively studied in the roundworm Caenorhabditis elegans. Here, we ask whether single-dose Cry5B can provide therapy against a hookworm infection and whether C. elegans mechanism-of-action studies are relevant to hookworms.
Methodology/Principal Findings
To test whether the C. elegans invertebrate-specific glycolipid receptor for Cry5B is relevant in hookworms, we fed Ancylostoma ceylanicum hookworm adults Cry5B with and without galactose, an inhibitor of Cry5B-C. elegans glycolipid interactions. As with C. elegans, galactose inhibits Cry5B toxicity in A. ceylanicum. Furthermore, p38 mitogen-activated protein kinase (MAPK), which controls one of the most important Cry5B signal transduction responses in C. elegans, is functionally operational in hookworms. A. ceylanicum hookworms treated with Cry5B up-regulate p38 MAPK and knock down of p38 MAPK activity in hookworms results in hypersensitivity of A. ceylanicum adults to Cry5B attack. Single-dose Cry5B is able to reduce by >90% A. ceylanicum hookworm burdens from infected hamsters, in the process eliminating hookworm egg shedding in feces and protecting infected hamsters from blood loss. Anthelmintic activity is increased about 3-fold, eliminating >97% of the parasites with a single 3 mg dose (∼30 mg/kg), by incorporating a simple formulation to help prevent digestion in the acidic stomach of the host mammal.
Conclusions/Significance
These studies advance the development of Cry5B protein as a potent, safe single-dose anthelmintic for hookworm therapy and make available the information of how Cry5B functions in C. elegans in order to study and improve Cry5B function against hookworms.
Author Summary
Hookworm infections are one of the great parasitic diseases of our time, infecting more than half a billion people worldwide and are a significant source of iron-deficient anemia. Although mass drug administrations to eliminate hookworms from children and pregnant women are being deployed, all the drugs for treatment we have lack full potency against the parasites and are showing signs of reduced efficacy. Crystal proteins, like Cry5B, made by Bacillus thuringiensis are as a class considered safe to vertebrates and have been shown to have efficacy against intestinal roundworms like hookworms. Here we show that the key mechanistic details of how Cry5B functions in hookworms is conserved with that of the model free-living roundworm Caenorhabditis elegans, which has implications for confirming Cry5B safety in vertebrates and for enhancing Cry5B efficacy against roundworms. Furthermore, we show that Cry5B works effectively as a single-dose drug against hookworm infections in hamsters and can be formulated to increase its efficacy, eliminating 97% of the parasites in a single dose. These results advance the development of a novel, safe single-dose therapy for hookworm infections in humans.
doi:10.1371/journal.pntd.0001900
PMCID: PMC3493396  PMID: 23145203
7.  Emergence of Proteus mirabilis Harboring blaKPC-2 and qnrD in a Chinese Hospital 
Nineteen carbapenem-nonsusceptible Proteus mirabilis isolates were recovered from intensive care units in the Second Affiliated Hospital of Zhejiang University during a 3-month period. The isolates showed a high level of resistance against ciprofloxacin, in addition to their resistance against the carbapenems. Pulsed-field gel electrophoresis (PFGE) analysis showed that these isolates belonged to three clonal strains. PCRs and DNA sequence analysis of the carbapenemase and other β-lactamase genes indicated that all the isolates harbored the blaKPC-2 gene. Twelve of 19 isolates harbored the plasmid-mediated quinolone resistance (PMQR) genes, both the qnrD and aac(6′)-Ib-cr genes. Eight representative isolates with high levels of quinolone resistance carried the similar mutation profiles of S83I in gyrA, E466D in gyrB, and S80I in parC. Reduced carbapenem susceptibility was transferred to Escherichia coli (EC600) in a conjugation experiment, while the quinolone resistance was not. DNA hybridization showed that qnrD was located on a plasmid of approximately 4.5 kb. In summary, large clonally related isolates of KPC-2-producing P. mirabilis emerged in a Chinese hospital, and qnrD was detected in KPC-producing P. mirabilis for the first time.
doi:10.1128/AAC.05519-11
PMCID: PMC3346625  PMID: 22354308
8.  Compromised Mitochondrial Fatty Acid Synthesis in Transgenic Mice Results in Defective Protein Lipoylation and Energy Disequilibrium 
PLoS ONE  2012;7(10):e47196.
A mouse model with compromised mitochondrial fatty acid synthesis has been engineered in order to assess the role of this pathway in mitochondrial function and overall health. Reduction in the expression of mitochondrial malonyl CoA-acyl carrier protein transacylase, a key enzyme in the pathway encoded by the nuclear Mcat gene, was achieved to varying extents in all examined tissues employing tamoxifen-inducible Cre-lox technology. Although affected mice consumed more food than control animals, they failed to gain weight, were less physically active, suffered from loss of white adipose tissue, reduced muscle strength, kyphosis, alopecia, hypothermia and shortened lifespan. The Mcat-deficient phenotype is attributed primarily to reduced synthesis, in several tissues, of the octanoyl precursors required for the posttranslational lipoylation of pyruvate and α-ketoglutarate dehydrogenase complexes, resulting in diminished capacity of the citric acid cycle and disruption of energy metabolism. The presence of an alternative lipoylation pathway that utilizes exogenous free lipoate appears restricted to liver and alone is insufficient for preservation of normal energy metabolism. Thus, de novo synthesis of precursors for the protein lipoylation pathway plays a vital role in maintenance of mitochondrial function and overall vigor.
doi:10.1371/journal.pone.0047196
PMCID: PMC3471957  PMID: 23077570
9.  Psychometric properties of the Chinese version of the Functional Assessment of Cancer Therapy-Cervix (FACT-Cx) measuring health-related quality of life 
Background
The Functional Assessment of Cancer Therapy (FACT) is one of the most commonly used self-report instruments for evaluation of health-related quality of life in oncology patients. However, cultural considerations necessitate testing of the subscales in different populations. We sought to qualitatively and quantitatively investigate the applicability and psychometric properties of the Chinese version of the FACT-Cervix (FACT-Cx) in Chinese women with cervical cancer.
Methods
Ten personal interviews were conducted in order to explore patients’ opinions about the scale and its items in depth. In addition the questionnaire was administered to 400 women with cervical cancer to test its psychometric properties. Reliability was assessed using Cronbach’s alpha coefficient and item-subscale correlation while validity was evaluated using factor analysis and known-group validity.
Results
Some items related to sex and the ability to give birth were questioned in the personal interviews, mostly regarding their significance and acceptance in the Chinese cultural context. The Cronbach’s alphas of FACT-Cx and the subscales were greater than 0.7, except for the cervical-cancer-specific subscale which was 0.57. Factor analysis demonstrated that the FACT-G construct generally paralleled the original. There were significant differences in the FACT-Cx and some subscales between those receiving and not receiving treatment and among the patients with different performance status.
Conclusions
In general, psychometric properties of the Chinese version supported its use with cervical cancer patients in Mainland China. Further work is needed to improve the psychometric adequacy of the cervical-cancer-specific subscale and adjust it to cultural considerations.
doi:10.1186/1477-7525-10-124
PMCID: PMC3503601  PMID: 23031680
Health-related quality of life; FACT-Cx; FACT-G; Chinese version; Psychometric properties; Cervical cancer
10.  Pno1 Tissue-Specific Expression and Its Functions Related to the Immune Responses and Proteasome Activities 
PLoS ONE  2012;7(9):e46093.
Pno1 is a protein that plays a role in proteasome and ribosome neogenesis in yeast. So far, its functions in mammalian cells have not been investigated. To understand its function in mammals, we performed in situ hybridization analysis of Pno1 expression in different development stages and generated Pno1 gene knockout (KO) and transgenic (Tg) mice lineages. The results showed early lethality of homozygous Pno1 KO lineage caused, as demonstrated in parallel by ex vivo experiments, by arrest of embryo development before compaction stage. Though, heterozygous (HET) mice with 50% of normal Pno1 mRNA concentration were fertile and showed no obvious anomalies. The lymphoid organs of HET mice were normal in size, weight and cellularity, with normal T and B cell subpopulations. TCR-triggered activation and proliferation of HET T cells were normal. Proteasome activities in HET organs were uncompromised. Tg mice with actin promoter-driven Pno1 expression were also fertile, with no apparent anomalies, although they expressed 2–5-fold higher Pno1 mRNA levels. The lymphoid organs of Tg mice were of normal size, weight and cellularity with normal T and B cell sub-populations. TCR-triggered activation and proliferation of Tg T cells were normal. Tg organs and tissues presented normal proteasome activity as did their wild type counterparts. Tagged Pno1 over-expression in L cells and density gradient fractionation established that Pno1 existed in large complexes with sedimentation rates between 20S and 26S, bigger than mature 26S proteasomes. Pno1 in fractions did not coincide with 40S or 60S ribosome subunits. Our study indicates that Pno1 is essential for cellular functions, but only a small percentage of its normal level is sufficient, and excessive amounts are neither harmful nor useful. The nature of the large complexes it associates with remains to be identified, but it is certain that they are not mature proteasomes or ribosomes.
doi:10.1371/journal.pone.0046093
PMCID: PMC3461026  PMID: 23029399
11.  An absence of both lamin B1 and lamin B2 in keratinocytes has no effect on cell proliferation or the development of skin and hair 
Human Molecular Genetics  2011;20(18):3537-3544.
Nuclear lamins are usually classified as A-type (lamins A and C) or B-type (lamins B1 and B2). A-type lamins have been implicated in multiple genetic diseases but are not required for cell growth or development. In contrast, B-type lamins have been considered essential in eukaryotic cells, with crucial roles in DNA replication and in the formation of the mitotic spindle. Knocking down the genes for B-type lamins (LMNB1, LMNB2) in HeLa cells has been reported to cause apoptosis. In the current study, we created conditional knockout alleles for mouse Lmnb1 and Lmnb2, with the goal of testing the hypothesis that B-type lamins are crucial for the growth and viability of mammalian cells in vivo. Using the keratin 14-Cre transgene, we bred mice lacking the expression of both Lmnb1 and Lmnb2 in skin keratinocytes (Lmnb1Δ/ΔLmnb2Δ/Δ). Lmnb1 and Lmnb2 transcripts were absent in keratinocytes of Lmnb1Δ/ΔLmnb2Δ/Δ mice, and lamin B1 and lamin B2 proteins were undetectable. But despite an absence of B-type lamins in keratinocytes, the skin and hair of Lmnb1Δ/ΔLmnb2Δ/Δ mice developed normally and were free of histological abnormalities, even in 2-year-old mice. After an intraperitoneal injection of bromodeoxyuridine (BrdU), similar numbers of BrdU-positive keratinocytes were observed in the skin of wild-type and Lmnb1Δ/ΔLmnb2Δ/Δ mice. Lmnb1Δ/ΔLmnb2Δ/Δ keratinocytes did not exhibit aneuploidy, and their growth rate was normal in culture. These studies challenge the concept that B-type lamins are essential for proliferation and vitality of eukaryotic cells.
doi:10.1093/hmg/ddr266
PMCID: PMC3159554  PMID: 21659336
12.  Fecal calprotectin levels are higher in rural than in urban Chinese infants and negatively associated with growth 
BMC Pediatrics  2012;12:129.
Background
Fecal calprotectin (FC) is an established simple biomarker of gut inflammation. To examine a possible relationship between linear growth and gut inflammation, we compared fecal calprotectin levels in 6 month old infants from poor rural vs affluent urban families.
Methods
The project was a cross-sectional comparison of FC from rural and urban populations in China. The relationship between length-for-age Z-score (LAZ) and FC concentrations were also compared. Single fecal samples were assayed for FC using EK-CAL ELISA kits.
Results
The age of subjects for both locations was 6.1 ± 0.2 mo; all were apparently healthy. The mean ± SD of the LAZ for the rural and urban infants were −0.6 ± 0.9 and 0.4 ± 0.9, respectively. FC had a non-normal distribution. The median FC of 420.9 and 140.1 μg/g for rural and urban infants, respectively, were significantly different (P < 0.0001). For the rural group, linear regression analysis showed that an increase in FC of 100 μg/g was associated with a decrease of 0.06 in LAZ.
Conclusion
FC levels were significantly elevated in the rural infants and high concentrations accounted for approximately one-third of the low LAZ scores of these infants.
doi:10.1186/1471-2431-12-129
PMCID: PMC3504525  PMID: 22917269
Fecal calprotectin; Infants; Children; Gut inflammation; Growth
13.  A summary index of infant and child feeding practices is associated with child growth in urban Shanghai 
BMC Public Health  2012;12:568.
Background
Recently, an infant and child feeding index (ICFI) constructed on brief recalls of breastfeeding, feeding frequency and food diversification was assumed to provide long-term prediction about child feeding practices. The aim of this study was to investigate the association between the cross-sectional ICFI (CS-ICFI) or longitudinal ICFI (L-ICFI) and child anthropometric indices in downtown Shanghai, China.
Methods
The prospective cohort study included 180 infants aged 5-7 mo with their main caregivers who were visited 3 times every 6 months over 12 months. A CS-ICFI was constructed for each visit by using data on feeding practices based on 24-h and 7-d recalls. An L-ICFI was constructed with use of the 3 CS-ICFIs. The associations between ICFI and length-for-age z score (LAZ), weight-for-age z score (WAZ), and weight-for-length z score (WLZ) were examined. The stability of the CS-ICFI was assessed by using repeatability coefficient (RC).
Results
The L-ICFI was positively associated with LAZ and WAZ at Visit 3(beta = 0.151, P = 0.040 and beta = 0.173, P = 0.024, respectively). Moreover, the CS-ICFI at Visit 1 was positively associated with LAZ, WAZ and WLZ (beta = 0.160, P = 0.029; beta = 0.191, P = 0.009; beta = 0.176, P = 0.020) at Visit 3, and the CS-ICFI at Visit 3 was also positively associated with LAZ (beta = 0.176, P = 0.016). Stability of the CS-ICFI was shown by the value of 0.14 (95% CI: 0.07, 0.31) of the RC, which differed significantly from 0 (P < 0.05).
Conclusions
The ICFI constructed on brief recalls based on cross-sectional studies can be used to evaluate the effects of child feeding practice on child growth.
doi:10.1186/1471-2458-12-568
PMCID: PMC3487749  PMID: 22839527
Child feeding practice; Brief recalls; Anthropometric indices; Repeatability coefficient
14.  The Apoptotic Function Analysis of p53, Apaf1, Caspase3 and Caspase7 during the Spermatogenesis of the Chinese Fire-Bellied Newt Cynops orientalis 
PLoS ONE  2012;7(6):e39920.
Background
Spontaneous and stress-induced germ cell apoptosis during spermatogenesis of multicellular organisms have been investigated broadly in mammals. Spermatogenetic process in urodele amphibians was essentially like that in mammals in spite of morphological differences; however, the mechanism of germ cell apoptosis in urodele amphibians remains unknown. The Chinese fire-belly newt, Cynops orientalis, was an excellent organism for studying germ cell apoptosis due to its sensitiveness to temperature, strong endurance of starvation, and sensitive skin to heavy metal exposure.
Methodology/Principal Findings
TUNEL result showed that spontaneous germ cell apoptosis took place in normal newt, and severe stress-induced apoptosis occurred to spermatids and sperm in response to heat shock (40°C 2 h), cold exposure(4°C 12 h), cadmium exposure(Cd 36 h), and starvation stress. Quantitative reverse transcription polymerase chain reactions (qRT-PCR) showed that gene expression of Caspase3 or Caspase7 was obviously elevated after stress treatment. Apaf1 was not altered at its gene expression level, and p53 was significantly decreased after various stress treatment. Caspase assay demonstrated that Caspase-3, -8,-9 enzyme activities in newt testis were significantly elevated after heat shock (40°C 2 h), cold exposure(4°C 12 h), and cadmium exposure(Cd 36 h), while Caspase3 and Caspase8 activities were increased with Caspase9 significantly decreased after starvation treatment.
Conclusions/Significance
Severe germ cell apoptosis triggered by heat shock, cold exposure, and cadmium exposure was Caspase3 dependent, which probably involved both extrinsic and intrinsic pathways. Apaf1 may be involved in this process without elevating its gene expression. But starvation-induced germ cell apoptosis was likely mainly through extrinsic pathway. p53 was probably not responsible for stress-induced germ cell apoptosis in newt testis. The intriguing high occurrence of spermatid and sperm apoptosis probably resulted from the sperm morphology and unique reproduction policy of Chinese fire-belly newt, Cynops orientalis.
doi:10.1371/journal.pone.0039920
PMCID: PMC3386923  PMID: 22768170
15.  Insights into interphase large-scale chromatin structure from analysis of engineered chromosome regions 
How chromatin folds into mitotic and interphase chromosomes has remained a difficult question for many years. We have used three generations of engineered chromosome regions as a means of visualizing specific chromosome regions in live cells and cells fixed under conditions which preserve large-scale chromatin structure. Our results confirm the existence of large-scale chromatin domains and fibers formed by the folding of 10 and 30 nm chromatin fibers into larger, spatially distinct domains. Transcription at levels within several fold of the levels measured for endogenous loci occur within these large-scale chromatin structures on a condensed template linearly compacted several hundred fold to one thousand fold relative to B-form DNA. However, transcriptional induction is accompanied by a several fold decondensation of this large-scale chromatin structure that propagates hundreds of kb beyond the induced gene. Examination of engineered chromosome regions in mouse ES and differentiated cells suggests a surprising degree of plasticity in this large-scale chromatin structure, allowing long-range DNA interactions within the context of large-scale chromatin fibers. Recapitulation of gene specific differences in large-scale chromatin conformation and nuclear positioning using these engineered chromosome regions will facilitate identification of cis and trans determinants of interphase chromosome architecture.
doi:10.1101/sqb.2010.75.050
PMCID: PMC3370657  PMID: 21467143
16.  In ovo leptin administration affects hepatic lipid metabolism and microRNA expression in newly hatched broiler chickens 
Background
A leptin-like immunoreactive substance has been found in chicken eggs and has been implicated in serving as a maternal signal to program offspring growth and metabolism. In the present study, we investigated the effects of in ovo leptin administration on hatch weight, serum and hepatic concentrations of metabolites and hormones, as well as on the expression of genes involved in hepatic lipid metabolism and the predicted microRNAs (miRNAs) targeting the affected genes. To this end we injected fertile eggs with either 0.5 μg of recombinant murine leptin or vehicle (PBS) before incubation.
Results
Prenatally leptin-exposed chicks showed lower hatch weight, but higher liver weight relative to the body weight, compared to the control group. In ovo leptin treatment increased the hepatic content and serum concentration of leptin in newly hatched chickens. The hepatic contents of triglycerides (TG) and total cholesterol (Tch) were decreased, whereas the serum levels of TG, Tch and apolipoprotein B (ApoB) were increased. The hepatic mRNA expression of sterol regulator element binding protein 1 (SREBP-1c), SREBP-2, hydroxy-3-methylglutaryl coenzyme A reductase (HMGCR) and cholesterol 7α-hydroxylase 1 (CYP7A1) was significantly up-regulated, as was the protein content of both SREBP-1c and SREBP-2 in hepatic nuclear extracts of leptin-treated chickens. Moreover, out of 12 miRNAs targeting SREBP-1c and/or HMGCR, five were significantly up-regulated in liver of leptin-treated chicks, including gga-miR-200b and gga-miR-429, which target both SREBP-1c and HMGCR.
Conclusions
These results suggest that leptin in ovo decreases hatch weight, and modifies hepatic leptin secretion and lipid metabolism in newly hatched broiler chickens, possibly via microRNA-mediated gene regulation.
doi:10.1186/2049-1891-3-16
PMCID: PMC3436634  PMID: 22958551
Broiler chickens; In ovo manipulation; Leptin; Lipid metabolism; Liver; MicroRNA; SREBPs
17.  Curcumin inhibits proliferation of human lens epithelial cells: a proteomic analysis*  
Objective: The incidence of after-cataracts [also known as posterior capsular opacification (PCO)] is between 30% and 50% three years following cataract surgery. Suppressing the proliferation of lens epithelial cells (LECs) is a primary goal in preventing PCO. Here, we investigated the proteomic regulation of the inhibitory effects of curcumin (Cur) on the proliferation of human lens epithelial B3 (HLE-B3) cells. Methods: Recombinant human basic fibroblast growth factor (rhbFGF) was used to induce proliferation of HLE-B3 cells, which were incubated with 20 mg/L Cur in a CO2 incubator for 24 h. Results: We found that the absorbance (A) value of rhbFGF group was significantly higher than the A value of the control group. Furthermore, the A value of the Cur group was significantly lower compared to the rhbFGF group, with an inhibition of 53.7%. Five different protein spots were obtained from proliferative HLE-B3 cells induced by rhbFGF. Eight different protein spots were obtained in HLE-B3 cells incubated with Cur. There were the common variational protein spots at mass/charge (m/z) ratios of 8 093 and 13 767 between rhbFGF group and control group as well as between the Cur group and rhbFGF group. Conclusions: These results show that Cur effectively inhibited HLE-B3 cell proliferation induced by rhbFGF. The protein spots at m/z of 8 093 and 13 767 may be the targets of Cur-induced inhibition of HLE-B3 cell proliferation. Cur may be a reliable and effective drug for prevention and treatment of polymerase chain reaction (PCR).
doi:10.1631/jzus.B1100278
PMCID: PMC3348232  PMID: 22556179
Curcumin; After-cataract; Posterior capsular opacification (PCO); Proteomics; Lens epithelial cells
18.  Combined Detection of Serum Matrix Metalloproteinase 9, Acetyl Heparinase and Cathepsin L in Diagnosis of Ovarian Cancer 
Objective
To investigate the clinic values of combining test of serum matrix metalloproteinase 9 (MMP-9), acetyl heparinase (Hpa) and Cathepsin L (CL) in diagnosis of ovarian cancer.
Methods
Serum levels of MMP-9, Hpa and CL were detected in a total of 418 cases, including 217 cases with ovarian malignant tumor, 100 cases with ovarian benign tumor and 101 healthy controls, by using enzyme-linked immunosorbent assay (ELISA). Their correlation with clinicopathologic feature of ovarian malignant tumor was analyzed and their diagnosis performance was evaluated by receiver operating characteristic (ROC). The combined diagnosis model was established by logistic regression analysis.
Results
The serum levels of MMP-9, Hpa and CL were significantly higher in patients with ovarian malignant tumor than in benign tumor and healthy control, the serum levels of CL and Hpa were higher in epithelial cancer than in non-epithelial tumor, and MMP-9, Hpa and CL were elevated in low grade and advanced stage compared to high grade and early stage. The sensitivity for diagnosis of ovarian malignant tumor from high to low was CL, Hpa and MMP-9, and the specificity was MMP-9, CL and Hpa. The united diagnosis model was established and showed the sensitivity and specificity of combined detection were 84.6% and 82.1%, respectively, which were significantly higher than a single tumor marker.
Conclusion
Serum MMP-9, Hpa and CL were correlated with ovarian malignant tumor and the combined detection of which may be valuable for clinical diagnosis of ovarian malignant tumor.
doi:10.1007/s11670-012-0067-1
PMCID: PMC3555258  PMID: 23359763
Ovarian cancer; Matrix metalloproteinase 9; Acetyl heparinase; Cathepsin; Diagnosis
19.  Novel MUC1 Aptamer Selectively Delivers Cytotoxic Agent to Cancer Cells In Vitro 
PLoS ONE  2012;7(2):e31970.
Chemotherapy is a primary treatment for cancer, but its efficacy is often limited by the adverse effects of cytotoxic agents. Targeted drug delivery may reduce the non-specific toxicity of chemotherapy by selectively directing anticancer drugs to tumor cells. MUC1 protein is an attractive target for tumor-specific drug delivery owning to its overexpression in most adenocarcinomas. In this study, a novel MUC1 aptamer is exploited as the targeting ligand for carrying doxorubicin (Dox) to cancer cells. We developed an 86-base DNA aptamer (MA3) that bound to a peptide epitope of MUC1 with a Kd of 38.3 nM and minimal cross reactivity to albumin. Using A549 lung cancer and MCF-7 breast cancer cells as MUC1-expressing models, MA3 was found to preferentially bind to MUC1-positive but not MUC1-negative cells. An aptamer-doxorubicin complex (Apt-Dox) was formulated by intercalating doxorubicin into the DNA structure of MA3. Apt-Dox was found capable of carrying doxorubicin into MUC1-positive tumor cells, while significantly reducing the drug intake by MUC1-negative cells. Moreover, Apt-Dox retained the efficacy of doxorubicin against MUC1-positive tumor cells, but lowered the toxicity to MUC1-negative cells (P<0.01). The results suggest that the MUC1 aptamer may have potential utility as a targeting ligand for selective delivery of cytotoxic agent to MUC1-expressing tumors.
doi:10.1371/journal.pone.0031970
PMCID: PMC3284512  PMID: 22384115
20.  The Pore-Forming Protein Cry5B Elicits the Pathogenicity of Bacillus sp. against Caenorhabditis elegans 
PLoS ONE  2011;6(12):e29122.
The soil bacterium Bacillus thuringiensis is a pathogen of insects and nematodes and is very closely related to, if not the same species as, Bacillus cereus and Bacillus anthracis. The defining characteristic of B. thuringiensis that sets it apart from B. cereus and B. anthracis is the production of crystal (Cry) proteins, which are pore-forming toxins or pore-forming proteins (PFPs). Although it is known that PFPs are important virulence factors since their elimination results in reduced virulence of many pathogenic bacteria, the functions by which PFPs promote virulence are incompletely understood. Here we study the effect of Cry proteins in B. thuringiensis pathogenesis of the nematode Caenorhabditis elegans. We find that whereas B. thuringiensis on its own is not able to infect C. elegans, the addition of the PFP Cry protein, Cry5B, results in a robust lethal infection that consumes the nematode host in 1–2 days, leading to a “Bob” or bag-of-bacteria phenotype. Unlike other infections of C. elegans characterized to date, the infection by B. thuringiensis shows dose-dependency based on bacterial inoculum size and based on PFP concentration. Although the infection process takes 1–2 days, the PFP-instigated infection process is irreversibly established within 15 minutes of initial exposure. Remarkably, treatment of C. elegans with Cry5B PFP is able to instigate many other Bacillus species, including B. anthracis and even “non-pathogenic” Bacillus subtilis, to become lethal and infectious agents to C. elegans. Co-culturing of Cry5B-expressing B. thuringiensis with B. anthracis can result in lethal infection of C. elegans by B. anthracis. Our data demonstrate that one potential property of PFPs is to sensitize the host to bacterial infection and further that C. elegans and probably other roundworms can be common hosts for B. cereus-group bacteria, findings with important ecological and research implications.
doi:10.1371/journal.pone.0029122
PMCID: PMC3245237  PMID: 22216181
21.  Selenium is a modulator of circadian clock that protects mice from the toxicity of a chemotherapeutic drug via upregulation of the core clock protein, BMAL1 
Oncotarget  2011;2(12):1279-1290.
Selenium compounds are known as cancer preventive agents and are also able to ameliorate the toxicity associated with anti-cancer radiation and chemotherapy in mouse models. Sensitivity to the toxicity of chemotherapy is also modulated by the circadian clock, molecular time-keeping system that underlie daily fluctuations in multiple physiological and biochemical processes. Here we show that these two mechanisms are interconnected. By screening a library of small molecules in a cell-based reporter system, we identified L-methyl-selenocysteine as a positive regulator of the core clock protein, BMAL1. L-methyl-selenocysteine up-regulates BMAL1 at the transcriptional level both in cultured cells and in mice. We also show that in tissue culture selenium exerts its action by interfering with TIEG1-mediated repression of Bmal1 promoter. Selenium treatment fails to protect BMAL1-deficient mice from toxicity induced by the chemotherapeutic agent cyclophosphamide but does protect Clock mutant mice deficient in circadian rhythm control but having normal BMAL1. These findings define selenium as circadian modulator and indicate that the tissue protective effect of selenium results, at least in part, from up-regulation of BMAL1 expression and subsequent enhancement of CLOCK/BMAL1-mediated transcription.
PMCID: PMC3282084  PMID: 22249125
L-Methyl-selenocysteine; TIEG1; circadian rhythms; cyclophosphamide; anticancer treatment; liver; transcription
22.  The structural stability and chaperone activity of artemin, a ferritin homologue from diapause-destined Artemia embryos, depend on different cysteine residues 
Cell Stress & Chaperones  2010;16(2):133-141.
Diapause-destined embryos of the crustacean, Artemia franciscana, accumulate large amounts of an oligomeric, heat-stable, molecular chaperone termed artemin, a cysteine-enriched ferritin homologue. In this study, cysteines 22, 61, 166, and 172 of artemin were substituted with alanines, respectively yielding ArtC22A, ArtC61A, ArtC166A, and ArtC172A. Wild-type and modified artemins were synthesized in transformed bacteria and purified. As measured by heat-induced denaturation of citrate synthase in vitro, each substitution reduced chaperone activity, with ArtC172A the least active. Protein modeling indicated that C172 is close to a region of surface hydrophobicity, also present in ferritin, suggesting that this site contributes to chaperone activity. Only slight differences in oligomer molecular mass were apparent between artemin variants, but ArtC22A and ArtC61A displayed significantly reduced thermostability, perhaps due to the disruption of an inter-subunit disulphide bridge. In contrast, ArtC172A was thermostable, reflecting the location of C172 on the oligomer surface and that it contributes minimally to artemin stabilization. To our knowledge, this is the initial study of structure/function relationships within a ferritin homologue of importance in diapause and the first to indicate that a defined region of hydrophobicity contributes to artemin and ferritin chaperoning.
doi:10.1007/s12192-010-0225-7
PMCID: PMC3059798  PMID: 20878295
Artemin; Ferritin homologue; Molecular chaperone; Diapause; Protein structure/function; Cysteine; Artemia franciscana
23.  Novel Aptamer-Nanoparticle Bioconjugates Enhances Delivery of Anticancer Drug to MUC1-Positive Cancer Cells In Vitro 
PLoS ONE  2011;6(9):e24077.
MUC1 protein is an attractive target for anticancer drug delivery owing to its overexpression in most adenocarcinomas. In this study, a reported MUC1 protein aptamer is exploited as the targeting agent of a nanoparticle-based drug delivery system. Paclitaxel (PTX) loaded poly (lactic-co-glycolic-acid) (PLGA) nanoparticles were formulated by an emulsion/evaporation method, and MUC1 aptamers (Apt) were conjugated to the particle surface through a DNA spacer. The aptamer conjugated nanoparticles (Apt-NPs) are about 225.3 nm in size with a stable in vitro drug release profile. Using MCF-7 breast cancer cell as a MUC1-overexpressing model, the MUC1 aptamer increased the uptake of nanoparticles into the target cells as measured by flow cytometry. Moreover, the PTX loaded Apt-NPs enhanced in vitro drug delivery and cytotoxicity to MUC1+ cancer cells, as compared with non-targeted nanoparticles that lack the MUC1 aptamer (P<0.01). The behavior of this novel aptamer-nanoparticle bioconjugates suggests that MUC1 aptamers may have application potential in targeted drug delivery towards MUC1-overexpressing tumors.
doi:10.1371/journal.pone.0024077
PMCID: PMC3164674  PMID: 21912664
24.  Mechanisms of inhibition of elemene on human lens epithelial cell proliferation in vitro 
AIM
To study the effects of elemene (Ele) on proliferation and cell cycle of human lens epithelial cells B3 (HLE-B3) and the mechanisms of its signal transduction.
METHODS
Recombinant human basic fibroblast growth factor (rhbFGF) was used to induce proliferation of HLE-B3 cells, which were incubated with 80mg/L Ele for 24 hours. The inhibitory effects of Ele on the proliferation of HLE-B3 cells were evaluated by MTT method. The effect of Ele on HLE-B3 cell cycle was analyzed by flow cytometry(FCM). The expressions of protein kinase A (PKA) and protein kinase G (PKG) of HLE-B3 were also analyzed by FCM.
RESULTS
Ele altered the cell cycle of HLE-B3 and effectively inhibited HLE-B3 cell proliferation induced by rhbFGF. Ele up-regulated PKA and down-regulated the expression of PKG in HLE-B3 cell.
CONCLUSION
Ele inhibits HLE-B3 proliferation, making it an attractive potential agent in regimens to treat after-cataracts.
doi:10.3980/j.issn.2222-3959.2011.03.08
PMCID: PMC3340820  PMID: 22553656
lens epithelial cell; cell culture; after-cataract; elemene
25.  Hsp70 gene association with nuclear speckles is Hsp70 promoter specific 
The Journal of Cell Biology  2010;191(4):711-719.
An Hsp70 transgene system is used to identify cis-elements required for gene-specific association with nuclear speckles.
Many mammalian genes localize near nuclear speckles, nuclear bodies enriched in ribonucleic acid–processing factors. In this paper, we dissect cis-elements required for nuclear speckle association of the heat shock protein 70 (Hsp70) locus. We show that speckle association is a general property of Hsp70 bacterial artificial chromosome transgenes, independent of the chromosome integration site, and can be recapitulated using a 2.8-kilobase HSPA1A gene fragment. Association of Hsp70 transgenes and their transcripts with nuclear speckles is transcription dependent, independent of the transcribed sequence identity, but dependent on the Hsp70 promoter sequence. Transgene speckle association does not correlate with the amount of transcript accumulation, with large transgene arrays driven by different promoters showing no speckle association, but smaller Hsp70 transgene arrays with lower transcript accumulation showing high speckle association. Moreover, despite similar levels of transcript accumulation, Hsp70 transgene speckle association is observed after heat shock but not cadmium treatment. We suggest that certain promoters may direct specific chromatin and/or transcript ribonucleoprotein modifications, leading to nuclear speckle association.
doi:10.1083/jcb.201004041
PMCID: PMC2983068  PMID: 21059845

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